| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/checkm_tree/checkm_tree/1.2.0+galaxy0 (this tool) |
| checkm_tree |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| checkm-genome | 1.2.0 | package |
| Additional information about this tool |
#import re
mkdir 'bins' &&
#if $bins.select == 'collection'
#for $b in $bins.bins_coll
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($b.element_identifier))
ln -s '$b.file_name' 'bins/${identifier}.fasta' &&
#end for
#else
#for $b in $bins.bins_ind
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($b.element_identifier))
ln -s '$b.file_name' 'bins/${identifier}.fasta' &&
#end for
#end if
checkm tree
'bins'
'output'
$reduced_tree
$ali
$nt
$genes
--extension 'fasta'
--threads \${GALAXY_SLOTS:-1}
--pplacer_threads \${GALAXY_SLOTS:-1}
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
bins|bins_coll: list collection bins|select: collection reduced_tree: True ali: False nt: False genes: False extra_outputs: genes_gff |
name: value name: value name: value name: value |
637000110.fna value |
| Test-2 |
bins|bins_coll: list collection bins|select: collection reduced_tree: True ali: True nt: False genes: False extra_outputs: ['hmmer_tree_ali', 'concatenate_pplacer_json', 'genes_faa'] |
name: value name: value name: value name: value name: value |
637000110.fna value |
| Test-3 |
bins|bins_coll: list collection bins|select: collection reduced_tree: True ali: False nt: True genes: False extra_outputs: genes_fna |
name: value name: value name: value name: value |
637000110.fna value |
| Test-4 |
bins|bins_coll: list collection bins|select: collection reduced_tree: True ali: False nt: False genes: True extra_outputs: |
name: value name: value name: value name: value |
637000110.faa value |